User:Wayne Decatur/kink-turn motif

WHEN MADE INTO AN OFFICIAL PAGE:
 * LINK FROM RNA motifs PAGE!!!!
 * Fix links from and to large ribosomal subunit (AND RIBOSOME?) page
 * Fix link from topic pages and from table of contents
 * add Redirect from K-turn motif
 * add redirect from GA motif
 * add redirect from kink-turn
 * add redirect from k-turn

The kink-turn motif A common RNA structural motif that consists of helix–internal loop–helix motif that introduces a very tight kink into the helical axis.

Introduction
The kink-turn motif is a common RNA structural motif that consists of helix–internal loop–helix motif that introduces a very tight kink into the helical axis, as illustrated in the figure below and 3D structure window on the right. Originally identified in the course of analyzing the large ribosomal subunit, this RNA structural motif was also identified in other RNAs. Particular instances have been called the GA motif.



The kink-turn motif includes the A-minor motif. Many kink-turns bind proteins; however, that trait is not universal. They can mediate RNA tertiary structure interactions as well.

An excellent introduction can be found here as part of a structural database for k-turn motifs in RNA by the Lilley group.

Structures Containing the Motif

 * The Large Ribosomal Subunit:
 * The Large Ribosomal Subunit contains 9 identified kink-turns : Kt-7 and Kt-7 with bound proteins ; Kt-15 and Kt-15 with bound proteins ; Kt-38 ; Kt-42 and Kt-42 with bound proteins ; Kt-46 and Kt-46 with bound proteins ); Kt-58 and Kt-58 with bound proteins ; Kt-4/5 and Kt-4/5 with bound protein ; Kt-94/99 and Kt-94/99 with bound protein of 3cc2; Kt-78 as observed in 2wh2 (While present based on sequence comparison, Kt-78 is in a portion of the large subunit not visible in the crystal structure of 3cc2.)
 * <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns/7'>The location of the eight kink-turns observed in the solved structure of the Haloarcula large ribosomal subunit shows they are on the surface of the subunit: <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt7/1'>Kt-7, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt15/1'>Kt-15 , <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns/8'>Kt-38 , <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt42/1'>Kt-42 , <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt46/1'>Kt-46 , <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt58/1'>Kt-58 , <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns4slash5/1'>Kt-4/5 , and <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns94slash99/2'>Kt-94/99 .   (A ninth kink-turn, Kt-78, though present in Haloarcula marismortui rRNA is in a portion not resolved in the actual Haloarcula marismortui structure, yet is also on the surface.)
 * See all of the 23S rRNA kink-turns and others on this page in greater detail following the appropriate links on this page at a structural database for k-turn motifs in RNA by the Lilley group.


 * The human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to the kink-turn of a U4 spliceosomal RNA fragment (1e7k) . The fact both the box C/D small nucleolar RNAs and the spliceosomal U4 RNA share this motif, and in fact bind the same protein, was observed even before the kink-turn was shown to be a widespread RNA motif.
 * The <scene name='User:Wayne_Decatur/kink-turn_motif/Proteincolored/1'>box C/D RNP from Sulfolobus solfataricus has two kink-turns that are bound by L7Ae (3pla) ..
 * A. fulgidus small ribonucleoprotein particle box C/D RNA has a kink-turn that is bound by L7Ae (1rlg) has a kink turn.
 * Pyrococcus furiosus small ribonucleoprotein particle box H/ACA RNA (2hvy ,3hax,3hay ) has a kink turn that is bound directly by L7ae in a complex of several proteins.
 * Azoarcus group I intron:
 * The Azoarcus group I intron (1u6b, 1zzn, 3bo2, 3bo3, 3bo4, and 3iin)   has a 'reverse' kink-turn. Overlay of the Azoarcus group I intron reverse kink-turn with a typical one (Kt-7) clearly illustrates the difference. PUT A SCENE HERE OF ALIGNMENT OF THIS WITH KT-7 with each Kt colored differently
 * <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns/7'>The location of the single kink-turn highlighted within the solved structure of theAzoarcus group I intron.


 * S. cerevisiae L30e bound to its pre-mRNA (1t0k) has a kink-turn with a protein bound.
 * S-adenosylmethionine riboswitch regulatory mRNA element from Thermoanaerobacter tengcongensis (2gis) has a kink-turn.
 * The lysine riboswitch regulatory mRNA element from  Thermotoga maritima (3dox) has a kink-turn
 * 1nkw – The Large Ribosomal Subunit From Deinococcus radiodurans
 * The small ribosomal subunit (2wh1) has two kink-turns.

Additional Literature and External Resources

 * Kink-turns in RNA - a structural database for k-turn motifs in RNA by the Lilley group